AutoCloner

Multiple sequence alignment - TraesCS3B01G236800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS3B01G236800	chr3B	100.000	3274	0	0	1	3274	370212559	370215832	0.000000e+00	6047.0
1	TraesCS3B01G236800	chr3B	93.613	1957	114	8	1323	3274	763485553	763483603	0.000000e+00	2911.0
2	TraesCS3B01G236800	chr5D	94.399	1964	93	9	1321	3274	44511941	44513897	0.000000e+00	3001.0
3	TraesCS3B01G236800	chr5D	77.964	835	132	29	325	1124	517218375	517219192	2.960000e-130	475.0
4	TraesCS3B01G236800	chrUn	94.679	1917	89	8	1366	3274	43407879	43409790	0.000000e+00	2963.0
5	TraesCS3B01G236800	chr2D	94.079	1959	89	14	1326	3274	84780830	84782771	0.000000e+00	2950.0
6	TraesCS3B01G236800	chr2D	93.763	1956	99	13	1326	3272	645082450	645080509	0.000000e+00	2915.0
7	TraesCS3B01G236800	chr4D	93.887	1963	104	11	1320	3274	78732772	78730818	0.000000e+00	2946.0
8	TraesCS3B01G236800	chr6D	93.133	1966	105	12	1325	3274	12108135	12106184	0.000000e+00	2856.0
9	TraesCS3B01G236800	chr5A	92.668	1964	125	12	1320	3274	650703525	650701572	0.000000e+00	2811.0
10	TraesCS3B01G236800	chr5A	92.627	1953	112	19	1321	3259	702815062	702813128	0.000000e+00	2780.0
11	TraesCS3B01G236800	chr3D	91.736	1331	82	11	1	1322	279879626	279878315	0.000000e+00	1823.0
12	TraesCS3B01G236800	chr5B	76.790	922	160	34	291	1179	649509291	649510191	4.950000e-128	468.0
13	TraesCS3B01G236800	chr5B	84.776	335	45	3	289	623	649699563	649699891	6.770000e-87	331.0
14	TraesCS3B01G236800	chr1B	90.196	51	5	0	175	225	456610	456560	2.110000e-07	67.6

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS3B01G236800	chr3B	370212559	370215832	3273	False	6047	6047	100.000	1	3274	1	chr3B.!!$F1	3273
1	TraesCS3B01G236800	chr3B	763483603	763485553	1950	True	2911	2911	93.613	1323	3274	1	chr3B.!!$R1	1951
2	TraesCS3B01G236800	chr5D	44511941	44513897	1956	False	3001	3001	94.399	1321	3274	1	chr5D.!!$F1	1953
3	TraesCS3B01G236800	chr5D	517218375	517219192	817	False	475	475	77.964	325	1124	1	chr5D.!!$F2	799
4	TraesCS3B01G236800	chrUn	43407879	43409790	1911	False	2963	2963	94.679	1366	3274	1	chrUn.!!$F1	1908
5	TraesCS3B01G236800	chr2D	84780830	84782771	1941	False	2950	2950	94.079	1326	3274	1	chr2D.!!$F1	1948
6	TraesCS3B01G236800	chr2D	645080509	645082450	1941	True	2915	2915	93.763	1326	3272	1	chr2D.!!$R1	1946
7	TraesCS3B01G236800	chr4D	78730818	78732772	1954	True	2946	2946	93.887	1320	3274	1	chr4D.!!$R1	1954
8	TraesCS3B01G236800	chr6D	12106184	12108135	1951	True	2856	2856	93.133	1325	3274	1	chr6D.!!$R1	1949
9	TraesCS3B01G236800	chr5A	650701572	650703525	1953	True	2811	2811	92.668	1320	3274	1	chr5A.!!$R1	1954
10	TraesCS3B01G236800	chr5A	702813128	702815062	1934	True	2780	2780	92.627	1321	3259	1	chr5A.!!$R2	1938
11	TraesCS3B01G236800	chr3D	279878315	279879626	1311	True	1823	1823	91.736	1	1322	1	chr3D.!!$R1	1321
12	TraesCS3B01G236800	chr5B	649509291	649510191	900	False	468	468	76.790	291	1179	1	chr5B.!!$F1	888

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
250	251	0.462759	GCTGTAGGACCACATGCTCC	60.463	60.0	0.00	0.0	0.0	4.70	F
1001	1030	0.100682	CGCCTAGTACTGCACACGAT	59.899	55.0	5.39	0.0	0.0	3.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1631	1678	0.250945	TCTCTCTCGCTGTGGTCACT	60.251	55.0	2.66	0.00	0.00	3.41	R
2882	2954	0.644843	CGCACCAACTTTTTGTGCAC	59.355	50.0	10.75	10.75	38.56	4.57	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	8.259411	TCCACTTGTACTTGTCTGTAACTAAAA	58.741	33.333	0.00	0.00	0.00	1.52
28	29	8.333186	CCACTTGTACTTGTCTGTAACTAAAAC	58.667	37.037	0.00	0.00	0.00	2.43
85	86	3.839490	TGGGAAGTATCGTTTTAGACCCA	59.161	43.478	0.00	0.00	41.81	4.51
139	140	7.063308	ACAAAATGTCACAGTGTTTGAAATGTC	59.937	33.333	17.09	0.00	34.16	3.06
245	246	1.071699	ACGTTTGCTGTAGGACCACAT	59.928	47.619	0.00	0.00	0.00	3.21
250	251	0.462759	GCTGTAGGACCACATGCTCC	60.463	60.000	0.00	0.00	0.00	4.70
252	253	2.388735	CTGTAGGACCACATGCTCCTA	58.611	52.381	9.39	9.39	38.01	2.94
270	271	5.746245	GCTCCTATTATACAAGCTAGCATCG	59.254	44.000	18.83	7.01	0.00	3.84
309	310	8.324306	TGCAGGCTGCTAAGATATTTTCTATAT	58.676	33.333	36.50	0.00	45.31	0.86
341	342	6.374053	CCCCTTGAAAATTCAAAACAACAGTT	59.626	34.615	9.63	0.00	45.61	3.16
471	474	5.036117	AGGCACACTTTTCAGAACTCTTA	57.964	39.130	0.00	0.00	0.00	2.10
594	597	8.296000	TCATATAATGACAACACACCAAGTTTG	58.704	33.333	0.00	0.00	33.59	2.93
603	606	6.589907	ACAACACACCAAGTTTGAAGAATTTC	59.410	34.615	0.00	0.00	0.00	2.17
681	687	1.402456	GGGTGACACACGCTACTAGTG	60.402	57.143	5.39	0.00	42.71	2.74
732	738	1.161563	ACGTGGTTGGCGTTTGGTAG	61.162	55.000	0.00	0.00	39.79	3.18
762	768	1.323534	CACGTACATTAGCAGCGTTCC	59.676	52.381	0.00	0.00	33.28	3.62
763	769	1.067425	ACGTACATTAGCAGCGTTCCA	60.067	47.619	0.00	0.00	31.37	3.53
765	771	2.222729	CGTACATTAGCAGCGTTCCAAC	60.223	50.000	0.00	0.00	0.00	3.77
784	799	4.158384	CAACATCGCACAAGTTGTTATCC	58.842	43.478	5.57	0.00	38.20	2.59
834	849	4.513406	TTTATTAACTTCCCGCTCCCAT	57.487	40.909	0.00	0.00	0.00	4.00
853	868	4.382901	CCCATGAACTCTCTCTTCTTCCTG	60.383	50.000	0.00	0.00	0.00	3.86
891	906	2.239400	TCTCTCTCTTTCTTCACCGCA	58.761	47.619	0.00	0.00	0.00	5.69
937	952	1.523758	GACCGCTGGACTTTTGACAT	58.476	50.000	1.50	0.00	0.00	3.06
938	953	1.197721	GACCGCTGGACTTTTGACATG	59.802	52.381	1.50	0.00	0.00	3.21
949	965	5.584649	GGACTTTTGACATGGACGATCATTA	59.415	40.000	0.00	0.00	0.00	1.90
967	983	1.884075	TAGTGGCATTCGTGTCCGCT	61.884	55.000	0.00	0.00	42.69	5.52
1000	1029	1.239296	ACGCCTAGTACTGCACACGA	61.239	55.000	5.39	0.00	0.00	4.35
1001	1030	0.100682	CGCCTAGTACTGCACACGAT	59.899	55.000	5.39	0.00	0.00	3.73
1421	1463	0.673333	CTAGTCCATGCGCACCAACA	60.673	55.000	14.90	0.00	0.00	3.33
1423	1465	2.112928	TCCATGCGCACCAACACT	59.887	55.556	14.90	0.00	0.00	3.55
1518	1560	2.238646	ACGGCCAATTCTATTCAGACCA	59.761	45.455	2.24	0.00	0.00	4.02
1556	1598	1.214062	GACCCAGCAGAGAGTCGTG	59.786	63.158	0.00	0.00	0.00	4.35
1631	1678	2.340078	GTGACAGAGAGCACGGCA	59.660	61.111	0.00	0.00	0.00	5.69
1664	1719	4.863925	GAGAGAGAGCACGGCGGC	62.864	72.222	13.24	12.27	0.00	6.53
1739	1794	2.500910	CTCCATGTCTTCCTCAAGCTCT	59.499	50.000	0.00	0.00	0.00	4.09
1800	1855	0.315568	GCCTGTCTTCGTCTGTCTGT	59.684	55.000	0.00	0.00	0.00	3.41
1808	1863	2.734591	GTCTGTCTGTGGTGCCGA	59.265	61.111	0.00	0.00	0.00	5.54
1840	1895	0.393077	CGGAGGGTTTCTCACACACT	59.607	55.000	0.00	0.00	44.19	3.55
1894	1950	2.223971	GCGAGAATGGGGTAAGAATCGA	60.224	50.000	0.00	0.00	0.00	3.59
1990	2046	2.814336	GCTTCTTTCTTTGGGTCGATGT	59.186	45.455	0.00	0.00	0.00	3.06
2129	2185	0.179113	GCACTGACAGAGAGCTAGCC	60.179	60.000	12.13	2.81	35.53	3.93
2167	2223	4.287766	TGAAGAAGAAGGTTAGGAAGCC	57.712	45.455	0.00	0.00	0.00	4.35
2339	2396	8.472007	TCACCTAGTTTAAATGTTGGTCAAAT	57.528	30.769	0.00	0.00	0.00	2.32
2347	2404	9.833182	GTTTAAATGTTGGTCAAATTTGTTTGT	57.167	25.926	17.47	0.00	33.82	2.83
2349	2406	9.831737	TTAAATGTTGGTCAAATTTGTTTGTTG	57.168	25.926	17.47	0.00	33.82	3.33
2350	2407	7.678947	AATGTTGGTCAAATTTGTTTGTTGA	57.321	28.000	17.47	0.00	33.82	3.18
2453	2517	4.541973	TGAAATGCAACTCTCTGCTCTA	57.458	40.909	0.00	0.00	43.07	2.43
2498	2564	1.425066	TCTGTGGGCCAAATTCAGAGT	59.575	47.619	17.81	0.00	32.49	3.24
2556	2622	2.862541	CATCCAATTAGGCCCATTCGA	58.137	47.619	0.00	0.00	37.29	3.71
2586	2654	5.465935	TCTTGCGTGTTTTTCTGTTTTCTT	58.534	33.333	0.00	0.00	0.00	2.52
2634	2702	6.421801	ACTCATAATGCTGAAACTTTTTGTGC	59.578	34.615	0.00	0.00	0.00	4.57
2678	2746	8.306761	CCAGAGCCAAACAATTAAGTTTAGAAT	58.693	33.333	0.00	0.00	39.55	2.40
2882	2954	6.490040	TGTCTAGAAAAATGAAGGGTGGAAAG	59.510	38.462	0.00	0.00	0.00	2.62
2893	2965	2.168313	AGGGTGGAAAGTGCACAAAAAG	59.832	45.455	21.04	0.00	40.73	2.27
2979	3051	2.119495	ACCGCTAGGACAGATGGAAAT	58.881	47.619	0.00	0.00	41.02	2.17
3079	3151	5.557891	TTGTTTTGCACTGAAATTTTGGG	57.442	34.783	0.00	0.00	0.00	4.12
3203	3279	5.375417	TTGCATGTTAGTTCATGACTTGG	57.625	39.130	10.28	0.00	45.41	3.61
3209	3285	7.306749	GCATGTTAGTTCATGACTTGGTTTTTG	60.307	37.037	10.28	0.00	45.41	2.44
3210	3286	7.164230	TGTTAGTTCATGACTTGGTTTTTGT	57.836	32.000	0.00	0.00	39.86	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
65	66	5.082251	AGTGGGTCTAAAACGATACTTCC	57.918	43.478	0.00	0.00	0.00	3.46
66	67	7.599998	TGTAAAGTGGGTCTAAAACGATACTTC	59.400	37.037	0.00	0.00	30.50	3.01
67	68	7.444299	TGTAAAGTGGGTCTAAAACGATACTT	58.556	34.615	0.00	0.00	31.45	2.24
68	69	6.996509	TGTAAAGTGGGTCTAAAACGATACT	58.003	36.000	0.00	0.00	0.00	2.12
69	70	7.838771	ATGTAAAGTGGGTCTAAAACGATAC	57.161	36.000	0.00	0.00	0.00	2.24
70	71	8.851541	AAATGTAAAGTGGGTCTAAAACGATA	57.148	30.769	0.00	0.00	0.00	2.92
71	72	7.754851	AAATGTAAAGTGGGTCTAAAACGAT	57.245	32.000	0.00	0.00	0.00	3.73
72	73	7.499895	AGAAAATGTAAAGTGGGTCTAAAACGA	59.500	33.333	0.00	0.00	0.00	3.85
73	74	7.645402	AGAAAATGTAAAGTGGGTCTAAAACG	58.355	34.615	0.00	0.00	0.00	3.60
106	107	8.533965	CAAACACTGTGACATTTTGTATTTCTG	58.466	33.333	15.86	0.00	0.00	3.02
108	109	8.627487	TCAAACACTGTGACATTTTGTATTTC	57.373	30.769	15.86	0.00	0.00	2.17
110	111	8.994429	TTTCAAACACTGTGACATTTTGTATT	57.006	26.923	15.86	0.00	0.00	1.89
112	113	8.031864	ACATTTCAAACACTGTGACATTTTGTA	58.968	29.630	15.86	5.90	0.00	2.41
113	114	6.873076	ACATTTCAAACACTGTGACATTTTGT	59.127	30.769	15.86	6.90	0.00	2.83
114	115	7.276218	AGACATTTCAAACACTGTGACATTTTG	59.724	33.333	15.86	13.92	0.00	2.44
158	159	4.099824	CGTGTTTGGCGTTCTAAACTTTT	58.900	39.130	0.00	0.00	37.60	2.27
162	163	1.598601	TCCGTGTTTGGCGTTCTAAAC	59.401	47.619	0.00	0.00	37.32	2.01
245	246	6.611613	ATGCTAGCTTGTATAATAGGAGCA	57.388	37.500	17.23	0.00	41.26	4.26
250	251	7.875316	AACACGATGCTAGCTTGTATAATAG	57.125	36.000	17.23	2.04	0.00	1.73
252	253	8.244494	CATAACACGATGCTAGCTTGTATAAT	57.756	34.615	17.23	0.00	0.00	1.28
279	280	8.324306	AGAAAATATCTTAGCAGCCTGCATATA	58.676	33.333	20.53	10.56	40.01	0.86
282	283	5.383476	AGAAAATATCTTAGCAGCCTGCAT	58.617	37.500	20.53	5.95	40.01	3.96
309	310	9.686683	TGTTTTGAATTTTCAAGGGGATTTAAA	57.313	25.926	5.92	0.00	46.68	1.52
380	381	6.659745	AGTTTGTTGGCATATCATATGCAT	57.340	33.333	27.28	3.79	46.21	3.96
471	474	3.973206	TGTGTCACCACGAATAATCCT	57.027	42.857	0.00	0.00	44.92	3.24
646	652	0.670162	CACCCAACCAAACTCTGCTG	59.330	55.000	0.00	0.00	0.00	4.41
681	687	2.044123	AATGTGGCTAAGGCTGTAGC	57.956	50.000	15.79	15.79	44.87	3.58
732	738	0.869730	AATGTACGTGGCGGTTTGTC	59.130	50.000	0.00	0.00	0.00	3.18
741	747	1.323534	GAACGCTGCTAATGTACGTGG	59.676	52.381	0.00	0.00	37.01	4.94
762	768	4.158384	GGATAACAACTTGTGCGATGTTG	58.842	43.478	10.86	10.86	42.67	3.33
763	769	3.120338	CGGATAACAACTTGTGCGATGTT	60.120	43.478	0.00	0.00	34.82	2.71
765	771	2.415168	ACGGATAACAACTTGTGCGATG	59.585	45.455	0.00	0.00	36.13	3.84
784	799	1.283736	GGACGGTTTGTATGCCTACG	58.716	55.000	0.00	0.00	0.00	3.51
834	849	3.829601	GGACAGGAAGAAGAGAGAGTTCA	59.170	47.826	0.00	0.00	0.00	3.18
853	868	1.213926	AGATGGCAAAGAGATGGGGAC	59.786	52.381	0.00	0.00	0.00	4.46
891	906	1.153369	CACGATGAGAATGGCGGGT	60.153	57.895	0.00	0.00	0.00	5.28
919	934	1.238439	CATGTCAAAAGTCCAGCGGT	58.762	50.000	0.00	0.00	0.00	5.68
937	952	3.466836	GAATGCCACTAATGATCGTCCA	58.533	45.455	0.00	0.00	0.00	4.02
938	953	2.476619	CGAATGCCACTAATGATCGTCC	59.523	50.000	0.00	0.00	0.00	4.79
949	965	2.742372	GCGGACACGAATGCCACT	60.742	61.111	0.00	0.00	44.60	4.00
991	1007	2.821366	GGAGGCCATCGTGTGCAG	60.821	66.667	5.01	0.00	0.00	4.41
1000	1029	1.470996	GCAGATCGAGAGGAGGCCAT	61.471	60.000	5.01	0.00	0.00	4.40
1001	1030	2.130426	GCAGATCGAGAGGAGGCCA	61.130	63.158	5.01	0.00	0.00	5.36
1262	1304	6.892658	AATTGGTTGCATACTCAAGTTGTA	57.107	33.333	2.11	0.00	0.00	2.41
1421	1463	0.600255	CGGCAGAGTTCACGGAAAGT	60.600	55.000	0.00	0.00	0.00	2.66
1423	1465	0.599204	GACGGCAGAGTTCACGGAAA	60.599	55.000	0.00	0.00	0.00	3.13
1518	1560	3.286751	ACAAGCCACGCGTGCAAT	61.287	55.556	33.17	17.72	41.40	3.56
1556	1598	2.817396	GCAACGGCTCTCTGCTCC	60.817	66.667	0.00	0.00	42.39	4.70
1631	1678	0.250945	TCTCTCTCGCTGTGGTCACT	60.251	55.000	2.66	0.00	0.00	3.41
1640	1687	1.089481	CGTGCTCTCTCTCTCTCGCT	61.089	60.000	0.00	0.00	0.00	4.93
1664	1719	0.390860	CCTCCACATCTAGCTTCCCG	59.609	60.000	0.00	0.00	0.00	5.14
1690	1745	1.602237	GAAGGGGATCTCAACGCCA	59.398	57.895	0.00	0.00	41.77	5.69
1840	1895	6.531503	AGAACGAATGATTCTAGTTCCTCA	57.468	37.500	16.88	0.00	41.28	3.86
1848	1903	4.796830	GCACACGTAGAACGAATGATTCTA	59.203	41.667	6.44	0.00	46.05	2.10
1894	1950	1.344114	ACGAAAATGGTGCAATTGCCT	59.656	42.857	26.94	7.00	41.18	4.75
1918	1974	1.358787	ACCCATTGCTCAAAGATCCCA	59.641	47.619	0.00	0.00	0.00	4.37
1990	2046	2.259917	TCATCAGAGTCTTGGCCAGAA	58.740	47.619	5.11	0.00	31.28	3.02
2129	2185	4.245660	TCTTCAACATCCTAAGCTCAACG	58.754	43.478	0.00	0.00	0.00	4.10
2167	2223	5.885230	TGGTATTTGTGCTTGATCTTCAG	57.115	39.130	0.00	0.00	0.00	3.02
2498	2564	1.003355	GCCTGCACTTGGCTCTACA	60.003	57.895	8.16	0.00	46.38	2.74
2556	2622	2.052782	AAAACACGCAAGAGAACCCT	57.947	45.000	0.00	0.00	43.62	4.34
2610	2678	6.421501	TGCACAAAAAGTTTCAGCATTATGAG	59.578	34.615	0.00	0.00	0.00	2.90
2634	2702	7.144000	GGCTCTGGAATAATTCAATTAGCTTG	58.856	38.462	0.00	0.00	36.09	4.01
2733	2802	7.747155	TTGGTCTTTGATTTAAATCACGGTA	57.253	32.000	26.69	12.35	44.54	4.02
2863	2935	4.058124	GCACTTTCCACCCTTCATTTTTC	58.942	43.478	0.00	0.00	0.00	2.29
2882	2954	0.644843	CGCACCAACTTTTTGTGCAC	59.355	50.000	10.75	10.75	38.56	4.57
2979	3051	3.521937	CCTTCCCTACCCATGTCAAAGTA	59.478	47.826	0.00	0.00	0.00	2.24
3079	3151	3.007398	TGCAAACATACATTTCCAACCCC	59.993	43.478	0.00	0.00	0.00	4.95
3203	3279	5.463392	GCCCTCTCTTTCATTCAACAAAAAC	59.537	40.000	0.00	0.00	0.00	2.43
3209	3285	4.331108	AGAAGCCCTCTCTTTCATTCAAC	58.669	43.478	0.00	0.00	0.00	3.18
3210	3286	4.583871	GAGAAGCCCTCTCTTTCATTCAA	58.416	43.478	6.23	0.00	46.32	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.